Magnetic Fe-B, Fe-Ni-B, and Co-B nanoparticles were successfully synthesized and introduced to water to prepare aqueous ferrofluids. The Fe-B, Fe-Ni-B, and Co-B particles are homogeneous amorphous nanoparticles with an average particle size 15 nm. The shape of the amorphous nanoparticles is regular. The Fe-B, Fe-Ni-B, and Co-B amorphous nanoparticles are superparamagnetic. Moreover, the saturation magnetizations of Fe-B and Fe-Ni-B amorphous nanoparticles are 75 emu/g and 51 emu/g. These are approximately 2.8 and 1.9-fold larger than Co-B nanoparticles, respectively. The viscosity of the amorphous ferrofluids has a strong response to external magnetic field. The yield stress increases with increasing magnetic field. The hyperthermia research of amorphous ferrofluids was firstly investigated. The experimental results indicate that the heating temperature of Fe-B ferrofluid and Fe-Ni-B ferrofluid could increase to 42 °C in 750 s and 960 s, respectively, when the output current is 300 A. The temperature could reach 61.6 °C for a Fe-B ferrofluid. The heating efficiencies of the amorphous ferrofluids demonstrate that the Fe-B ferrofluid and Fe-Ni-B ferrofluid may have great potential for biomedical applications.